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Protein

Isocitrate lyase

Gene

acuD

Organism
Emericella nidulans (strain FGSC A4 / ATCC 38163 / CBS 112.46 / NRRL 194 / M139) (Aspergillus nidulans)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Catalyzes the formation of succinate and glyoxylate from isocitrate, a key step of the glyoxylate cycle, which operates as an anaplerotic route for replenishing the tricarboxylic acid cycle. Required for growth on ethanol or acetate, but dispensable when fermentable carbon sources are available. Acts also on 2-methylisocitrate.By similarity

Catalytic activityi

Isocitrate = succinate + glyoxylate.By similarity
(2S,3R)-3-hydroxybutane-1,2,3-tricarboxylate = pyruvate + succinate.By similarity

Cofactori

Mg2+By similarity

Pathwayi: glyoxylate cycle

This protein is involved in step 1 of the subpathway that synthesizes (S)-malate from isocitrate.
Proteins known to be involved in the 2 steps of the subpathway in this organism are:
  1. Isocitrate lyase (acuD)
  2. Malate synthase, glyoxysomal (acuE)
This subpathway is part of the pathway glyoxylate cycle, which is itself part of Carbohydrate metabolism.
View all proteins of this organism that are known to be involved in the subpathway that synthesizes (S)-malate from isocitrate, the pathway glyoxylate cycle and in Carbohydrate metabolism.

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Metal bindingi168MagnesiumBy similarity1
Active sitei206Proton acceptor1 Publication1
Binding sitei243SubstrateBy similarity1
Binding sitei457SubstrateBy similarity1

GO - Molecular functioni

GO - Biological processi

  • acetate catabolic process Source: ASPGD
  • carbon utilization Source: ASPGD
  • fatty acid catabolic process Source: ASPGD
  • glyoxylate cycle Source: GO_Central
  • tricarboxylic acid cycle Source: UniProtKB-KW
Complete GO annotation...

Keywords - Molecular functioni

Lyase

Keywords - Biological processi

Glyoxylate bypass, Tricarboxylic acid cycle

Keywords - Ligandi

Magnesium, Metal-binding

Enzyme and pathway databases

UniPathwayiUPA00703; UER00719.

Names & Taxonomyi

Protein namesi
Recommended name:
Isocitrate lyase1 Publication (EC:4.1.3.1By similarity)
Short name:
ICLCurated
Short name:
IsocitraseCurated
Short name:
IsocitrataseCurated
Alternative name(s):
Methylisocitrate lyaseBy similarity (EC:4.1.3.30By similarity)
Short name:
MICACurated
Threo-D(S)-isocitrate glyoxylate-lyaseCurated
Gene namesi
Name:acuD1 Publication
ORF Names:AN5634
OrganismiEmericella nidulans (strain FGSC A4 / ATCC 38163 / CBS 112.46 / NRRL 194 / M139) (Aspergillus nidulans)
Taxonomic identifieri227321 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaPezizomycotinaEurotiomycetesEurotiomycetidaeEurotialesAspergillaceaeAspergillus
Proteomesi
  • UP000000560 Componenti: Chromosome V
  • UP000005890 Componenti: Partially assembled WGS sequence

Subcellular locationi

  • Glyoxysome By similarity

GO - Cellular componenti

  • glyoxysome Source: UniProtKB-SubCell
  • peroxisomal matrix Source: ASPGD
  • peroxisome Source: ASPGD
Complete GO annotation...

Keywords - Cellular componenti

Glyoxysome, Peroxisome

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000687901 – 538Isocitrate lyaseAdd BLAST538

Proteomic databases

PRIDEiP28298.

Interactioni

Subunit structurei

Homotetramer.1 Publication

Structurei

Secondary structure

1538
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi3 – 16Combined sources14
Helixi18 – 22Combined sources5
Helixi25 – 29Combined sources5
Helixi36 – 42Combined sources7
Helixi52 – 69Combined sources18
Beta strandi73 – 77Combined sources5
Helixi81 – 90Combined sources10
Beta strandi94 – 96Combined sources3
Helixi98 – 104Combined sources7
Helixi122 – 146Combined sources25
Helixi150 – 153Combined sources4
Beta strandi165 – 168Combined sources4
Beta strandi173 – 175Combined sources3
Helixi176 – 188Combined sources13
Beta strandi192 – 196Combined sources5
Beta strandi212 – 214Combined sources3
Helixi217 – 233Combined sources17
Beta strandi239 – 243Combined sources5
Helixi246 – 248Combined sources3
Beta strandi249 – 253Combined sources5
Helixi258 – 263Combined sources6
Beta strandi264 – 267Combined sources4
Helixi275 – 284Combined sources10
Helixi290 – 302Combined sources13
Helixi309 – 317Combined sources9
Helixi324 – 335Combined sources12
Helixi340 – 351Combined sources12
Beta strandi369 – 371Combined sources3
Helixi375 – 385Combined sources11
Beta strandi390 – 393Combined sources4
Helixi401 – 412Combined sources12
Beta strandi419 – 423Combined sources5
Beta strandi426 – 428Combined sources3
Helixi430 – 432Combined sources3
Helixi436 – 440Combined sources5
Helixi442 – 448Combined sources7
Beta strandi451 – 456Combined sources6
Helixi459 – 478Combined sources20
Helixi480 – 486Combined sources7
Helixi488 – 494Combined sources7
Helixi497 – 499Combined sources3
Helixi501 – 505Combined sources5
Helixi507 – 518Combined sources12

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1DQUX-ray2.80A1-538[»]
ProteinModelPortaliP28298.
SMRiP28298.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP28298.

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni97 – 99Substrate bindingBy similarity3
Regioni207 – 208Substrate bindingBy similarity2
Regioni423 – 427Substrate bindingBy similarity5

Sequence similaritiesi

Phylogenomic databases

HOGENOMiHOG000238475.
InParanoidiP28298.
KOiK01637.
OMAiVTEDQFH.
OrthoDBiEOG092C19UX.

Family and domain databases

Gene3Di3.20.20.60. 2 hits.
InterProiIPR006254. Isocitrate_lyase.
IPR018523. Isocitrate_lyase_ph_CS.
IPR015813. Pyrv/PenolPyrv_Kinase-like_dom.
[Graphical view]
PfamiPF00463. ICL. 1 hit.
[Graphical view]
SUPFAMiSSF51621. SSF51621. 1 hit.
TIGRFAMsiTIGR01346. isocit_lyase. 1 hit.
PROSITEiPS00161. ISOCITRATE_LYASE. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P28298-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSYIEEEDQR YWDEVAAVKN WWKDSRWRYT KRPFTAEQIV AKRGNLKIEY
60 70 80 90 100
PSNVQAKKLW GILERNFKNK EASFTYGCLD PTMVTQMAKY LDTVYVSGWQ
110 120 130 140 150
SSSTASSTDE PSPDLADYPM NTVPNKVNHL WMAQLFHDRK QREERMTTPK
160 170 180 190 200
DQRHKVANVD YLRPIIADAD TGHGGLTAVM KLTKLFVERG AAGIHIEDQA
210 220 230 240 250
PGTKKCGHMA GKVLVPISEH INRLVAIRAQ ADIMGTDLLA IARTDSEAAT
260 270 280 290 300
LITSTIDHRD HPFIIGSTNP DIQPLNDLMV MAEQAGKNGA ELQAIEDEWL
310 320 330 340 350
AKAGLKLFND AVVDAINNSP LPNKKAAIEK YLTQSKGKSN LEARAIAKEI
360 370 380 390 400
AGTDIYFDWE APRTREGYYR YQGGTQCAIN RAVAYAPFAD LIWMESKLPD
410 420 430 440 450
YKQAKEFADG VHAVWPEQKL AYNLSPSFNW KKAMPRDEQE TYIKRLGALG
460 470 480 490 500
YAWQFITLAG LHTTALISDT FAKAYAKQGM RAYGELVQEP EMANGVDVVT
510 520 530
HQKWSGANYV DNMLKMITGG VSSTAAMGKG VTEDQFKS
Length:538
Mass (Da):60,321
Last modified:May 1, 2007 - v3
Checksum:i21B5B56E5345681E
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti17Missing in CAA44572 (PubMed:1531185).Curated1
Sequence conflicti68Missing in CAA44572 (PubMed:1531185).Curated1
Sequence conflicti157A → T in CAA44572 (PubMed:1531185).Curated1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X62696 Genomic DNA. Translation: CAA44572.1.
AACD01000098 Genomic DNA. Translation: EAA62727.1.
BN001305 Genomic DNA. Translation: CBF81510.1.
PIRiS26857.
RefSeqiXP_663238.1. XM_658146.1.

Genome annotation databases

EnsemblFungiiCADANIAT00003436; CADANIAP00003436; CADANIAG00003436.
EAA62727; EAA62727; AN5634.2.
GeneIDi2871925.
KEGGiani:AN5634.2.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X62696 Genomic DNA. Translation: CAA44572.1.
AACD01000098 Genomic DNA. Translation: EAA62727.1.
BN001305 Genomic DNA. Translation: CBF81510.1.
PIRiS26857.
RefSeqiXP_663238.1. XM_658146.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1DQUX-ray2.80A1-538[»]
ProteinModelPortaliP28298.
SMRiP28298.
ModBaseiSearch...
MobiDBiSearch...

Proteomic databases

PRIDEiP28298.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblFungiiCADANIAT00003436; CADANIAP00003436; CADANIAG00003436.
EAA62727; EAA62727; AN5634.2.
GeneIDi2871925.
KEGGiani:AN5634.2.

Phylogenomic databases

HOGENOMiHOG000238475.
InParanoidiP28298.
KOiK01637.
OMAiVTEDQFH.
OrthoDBiEOG092C19UX.

Enzyme and pathway databases

UniPathwayiUPA00703; UER00719.

Miscellaneous databases

EvolutionaryTraceiP28298.

Family and domain databases

Gene3Di3.20.20.60. 2 hits.
InterProiIPR006254. Isocitrate_lyase.
IPR018523. Isocitrate_lyase_ph_CS.
IPR015813. Pyrv/PenolPyrv_Kinase-like_dom.
[Graphical view]
PfamiPF00463. ICL. 1 hit.
[Graphical view]
SUPFAMiSSF51621. SSF51621. 1 hit.
TIGRFAMsiTIGR01346. isocit_lyase. 1 hit.
PROSITEiPS00161. ISOCITRATE_LYASE. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiACEA_EMENI
AccessioniPrimary (citable) accession number: P28298
Secondary accession number(s): C8VFW4, Q5B1E6
Entry historyi
Integrated into UniProtKB/Swiss-Prot: December 1, 1992
Last sequence update: May 1, 2007
Last modified: November 30, 2016
This is version 126 of the entry and version 3 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.